Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- link to Sigma (or other company) page for assay or assay reagents (substrates)
Crotonoyl coenzyme A trilithium salt (for fabg)
28007-5MG -246.00 http://www.sigmaaldrich.com/catalog/search?interface=All&term=crotonoyl-CoA〈=en®ion=US&focus=product&N=0+220003048+219853269+219853286&mode=mode%20matchpartialmax
FabV (Enoyl-ACP Reductase)
NCBI Gene # or RefSeq#:
NZ_ACNR01000001.1
Protein ID (NP or XP #) or Wolbachia#:
ZP_04462052.1
Organism:
Yersinia Pestis biovar Orientalis str. India 195
Etiologic Risk Group (see link below):
India/Orientals
Background/Disease Information:
http://gsc.jcvi.org/projects/msc/yersinia/yersinia_pestis_biovar_orientalis_str_f1991016/index.shtml
http://gsc.jcvi.org/projects/msc/yersinia/yersinia_pestis_biovar_orientalis_str_ip275/index.shtml
http://gsc.jcvi.org/projects/msc/yersinia/yersinia_pestis_biovar_orientalis_str_mg05-1020/index.shtml
Cool link - Dr. B
Yersinia pestis study - old plague not different from new plague..
http://www.ncbi.nlm.nih.gov/pubmed/21993626
Essentiality of this protein:
http://www.ncbi.nlm.nih.gov/pubmed?term=fabv%20yersinia%20pestis
http://www.sciencedirect.com/science/article/pii/S0969212611004114
http://www.cell.com/structure/abstract/S0969-2126%2811%2900411-4
Complex of enzymes:
EC#: 1.3.1.-
Link to BRENDA EC# page:
http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.3.1.-
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay or assay reagents (substrates)
Crotonoyl coenzyme A trilithium salt (for fabg)
28007-5MG -246.00
http://www.sigmaaldrich.com/catalog/search?interface=All&term=crotonoyl-CoA〈=en®ion=US&focus=product&N=0+220003048+219853269+219853286&mode=mode%20matchpartialmax
-- link to paper that contains assay information
http://www.sciencedirect.com/science/article/pii/S0968089606008443
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model:
3ZU5
-- Query Coverage (if not direct match):
100%
-- Max Ident (if not direct match):
99%
Druggable Target (see Databases for this):
Current Inhibitors:
Expression Information (has it been expressed in bacterial cells):
Purification Method:
Image of protein (PyMol or etc):
Amino Acid Sequence:
MIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARIT AAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQL TIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESV LQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSI GAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVTQASSAIPMMPLYLSLLFKVMKEKG THEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQL TDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG
length of your protein in Amino Acids
399
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website
43346.0
Molar Extinction coefficient of your protein at 280 nm wavelength:
CDS Gene Sequence:
ATGATTATCAAGCCGCGTGTACGTGGTTTTATCTGTGTTACTGCGCATCCAACGGGTTGCGAGGCTAACGTGAAAAAACAGATCGACTACGTTACCACCGAAGGTCCGATTGCGAACGGTCCGAAACGTGTTCTGGTTATTGGTGCGTCTACCGGTTACGGTCTGGCAGCCCGTATCACGGCGGCTTTTGGTTGCGGCGCAGATACCCTGGGCGTTTTCTTCGAACGTCCTGGCGAAGAAGGCAAACCGGGTACGTCTGGTTGGTACAATTCTGCGGCGTTCCACAAATTCGCTGCGCAAAAAGGTCTGTACGCGAAATCTATCAACGGTGATGCGTTCTCTGACGAAATTAAGCAGCTCACCATTGACGCGATCAAACAGGACCTCGGTCAGGTTGACCAAGTTATTTACTCTCTCGCGTCTCCACGTCGTACCCACCCGAAGACCGGTGAAGTTTTCAACTCTGCGCTGAAACCTATTGGTAATGCTGTAAATCTGCGTGGCCTGGACACCGACAAAGAAGTTATCAAAGAATCTGTCCTGCAGCCGGCGACCCAGTCTGAAATCGACTCTACCGTTGCGGTCATGGGCGGTGAGGATTGGCAAATGTGGATCGATGCCCTCCTGGACGCGGGTGTTCTCGCGGAAGGTGCCCAAACCACCGCGTTCACCTACCTGGGTGAGAAAATCACGCACGATATCTATTGGAACGGTTCTATCGGTGCGGCGAAAAAAGACCTGGACCAGAAAGTTCTGGCGATCCGTGAATCTCTGGCGGCTCACGGTGGCGGCGATGCTCGTGTTTCTGTTCTGAAAGCGGTTGTTACCCAGGCGTCTTCTGCGATCCCTATGATGCCGCTCTACCTGTCTCTGCTGTTCAAAGTTATGAAAGAGAAAGGTACGCATGAAGGTTGCATCGAGCAGGTCTACTCCCTCTACAAAGATTCTCTGTGCGGTGATTCTCCGCACATGGACCAAGAAGGTCGTCTCCGTGCGGACTACAAGGAGCTCGACCCTGAAGTCCAGAATCAGGTTCAGCAGCTGTGGGACCAGGTGACCAACGACAACATCTACCAACTGACGGATTTCGTGGGTTACAAATCTGAATTCCTCAACCTCTTCGGTTTCGGTATCGACGGTGTTGACTACGACGCGGATGTTAACCCGGACGTCAAAATCCCGAATCTGATCCAGGGTTAA
GC% Content for gene:
52.5%
CDS Gene Sequence (codon optimized) - after having done Primer Design:
ATGATTATCAAGCCGCGTGTACGTGGTTTTATCTGTGTTACTGCGCATCCAACGGGTTGCGAGGCTAACGTGAAAAAACAGATCGACTACGTTACCACCGAAGGTCCGATTGCGAACGGTCCGAAACGTGTTCTGGTTATTGGTGCGTCTACCGGTTACGGTCTGGCAGCCCGTATCACGGCGGCTTTTGGTTGCGGCGCAGATACCCTGGGCGTTTTCTTCGAACGTCCTGGCGAAGAAGGCAAACCGGGTACGTCTGGTTGGTACAATTCTGCGGCGTTCCACAAATTCGCTGCGCAAAAAGGTCTGTACGCGAAATCTATCAACGGTGATGCGTTCTCTGACGAAATTAAGCAGCTCACCATTGACGCGATCAAACAGGACCTCGGTCAGGTTGACCAAGTTATTTACTCTCTCGCGTCTCCACGTCGTACCCACCCGAAGACCGGTGAAGTTTTCAACTCTGCGCTGAAACCTATTGGTAATGCTGTAAATCTGCGTGGCCTGGACACCGACAAAGAAGTTATCAAAGAATCTGTCCTGCAGCCGGCGACCCAGTCTGAAATCGACTCTACCGTTGCGGTCATGGGCGGTGAGGATTGGCAAATGTGGATCGATGCCCTCCTGGACGCGGGTGTTCTCGCGGAAGGTGCCCAAACCACCGCGTTCACCTACCTGGGTGAGAAAATCACGCACGATATCTATTGGAACGGTTCTATCGGTGCGGCGAAAAAAGACCTGGACCAGAAAGTTCTGGCGATCCGTGAATCTCTGGCGGCTCACGGTGGCGGCGATGCTCGTGTTTCTGTTCTGAAAGCGGTTGTTACCCAGGCGTCTTCTGCGATCCCTATGATGCCGCTCTACCTGTCTCTGCTGTTCAAAGTTATGAAAGAGAAAGGTACGCATGAAGGTTGCATCGAGCAGGTCTACTCCCTCTACAAAGATTCTCTGTGCGGTGATTCTCCGCACATGGACCAAGAAGGTCGTCTCCGTGCGGACTACAAGGAGCTCGACCCTGAAGTCCAGAATCAGGTTCAGCAGCTGTGGGACCAGGTGACCAACGACAACATCTACCAACTGACGGATTTCGTGGGTTACAAATCTGAATTCCTCAACCTCTTCGGTTTCGGTATCGACGGTGTTGACTACGACGCGGATGTTAACCCGGACGTCAAAATCCCGAATCTGATCCAGGGTTAA
GC% Content for gene (codon optimized):
52.5%
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
Primer design results for 'tail' primers (this is just 2 sequences):
Upstream
5’- TACTTCCAATCCATGATTATCAAGCCGCGT – 3’
Downstream
5’ – TATCCACCTTTACTGTTAACCCTGGATCAGATT – 3’
Primer Design Results
http://wwww.patricbrc.org/portal/portal/patric/Feature?cType=feature&cId=14081532
http://blast.ncbi.nlm.nih.gov/Blast.cgi
http://www.rcsb.org/pdb/explore/explore.do?structureId=3ZU5
LOGFileResults Primer Design
https://docs.google.com/open?id=0B4O2KqKh2q_-R1o0OEkwUEczWFU
<span style="color: #222222; font-size: 12px;">>lcl|45029[[#45029]] unnamed protein product Length=399 Score = 824 bits (2128), Expect = 0.0, Method: Compositional matrix adjust. Identities = 398/399 (99%), Positives = 399/399 (100%), Gaps = 0/399 (0%) Query 7 MIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARIT 66 MIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARIT Sbjct 1 MIIKPRVRGFICVTAHPTGCEANVKKQIDYVTTEGPIANGPKRVLVIGASTGYGLAARIT 60 Query 67 AAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQL 126 AAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQL Sbjct 61 AAFGCGADTLGVFFERPGEEGKPGTSGWYNSAAFHKFAAQKGLYAKSINGDAFSDEIKQL 120 Query 127 TIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESV 186 TIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESV Sbjct 121 TIDAIKQDLGQVDQVIYSLASPRRTHPKTGEVFNSALKPIGNAVNLRGLDTDKEVIKESV 180 Query 187 LQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSI 246 LQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSI Sbjct 181 LQPATQSEIDSTVAVMGGEDWQMWIDALLDAGVLAEGAQTTAFTYLGEKITHDIYWNGSI 240 Query 247 GAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVSQASSAIPMMPLYLSLLFKVMKEKG 306 GAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVV+QASSAIPMMPLYLSLLFKVMKEKG Sbjct 241 GAAKKDLDQKVLAIRESLAAHGGGDARVSVLKAVVTQASSAIPMMPLYLSLLFKVMKEKG 300 Query 307 THEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQL 366 THEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQL Sbjct 301 THEGCIEQVYSLYKDSLCGDSPHMDQEGRLRADYKELDPEVQNQVQQLWDQVTNDNIYQL 360 Query 367 TDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG 405 TDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG Sbjct 361 TDFVGYKSEFLNLFGFGIDGVDYDADVNPDVKIPNLIQG 399</span>